It’s been quite a while since college chemistry. Please refresh/update me!
How much slack is there where it comes to chemical bonds? In other words, in an idealized molecule, I imagine each bond/link as being basically frozen at equidistant points around the central atom. But in actual reality, I would think there’s some wiggle factor. Maybe the atoms can pretty much slide around nilly willy until their electron shell repels another one. And maybe each bond can freely revolve around the axis of that bond. But then I seem to remember in things like proteins, there isn’t just repulsion, there are also some non bond related attractions. How does that happen?
To sum up, how far can/does a typical (and special case) molecule tend to vary from it’s idealized structure?
There’s slack. Both electrostatic attraction/repulsion and the Pauli exclusion principle are “soft” in an ideal sense. The motions atoms experience approach the bond length in size, in the limit where thermal decomposition is about to occur. Room temperature is about 1/10 of the highest temperatures that chemical bonds can withstand, and the movements vary as the square root of temperature, so that gives you some idea of how wide the range of excursions is. The stretching and flexing and twisting of bonds is the origin of infrared absorption peaks in the spectra characteristic of chemical structures.
Well, not because of slackness per se, but because the slackness is not symmetrical in compression and expansion. When you pull bound atoms apart there is electrostatic force to resist you, but when you push them together you try to violate the Pauli exclusion principle. A graph of the potential energy in a bond therefore has a gradual slope as you stretch and a slope that becomes fantastically steep as you compress. IIRC this is often modeled as r^12, but this is just a handy approximation.
If you look up Lennard-Jones potential, you’ll see a graph.
So, at any temperature, the bond is stretching and compressing and getting equally high on the Lennard-Jones graph on both sides. If you try a hotter temperature, it gets higher on both sides.
The point is that because one side is more gradual and one side is steeper, the average distance gets bigger as you go higher up. The more gradual side dominates.